Metagenoms

Web sites

• NCBI Bacterial Genomes 647 Complete, 1067 in Progress
• JGI Fidelity of Analysis of Metagenomic Samples (FAMeS)
• JGI Simultaed High Complexity (SIMHC)
• Human Microbiome Project (HMP) @ NIH
• WUSTL Human Gut Microbiome (HGMI) 41 genomes
• Baylor HMP list of 353 genomes targeted for sequencing by the 4 centers
• JCVI HMP 50 genomes (oral,skin,vagina)
• JGI IMG
• HGMI at NIH
• HGMI TA ~150K Sanger traces; trimming points are given

Articles

• Kurokawa
• Gill
• JGI
• HMP Nature Oct 2007
• Human Microbiome Pilot Project (HMPP)
• Human Gut Microbiome Initiative (HGMI) Need for more RefSeqs; sequence the genomes of 100 cultured representatives of the phylogenetic diversity in the human gut microbiota
• Nature Reviews: Microbiology in the post-genomic era
• IMG NAR 2007

HMP

NIH Roadmap

1. Sequence the genomes of 200 microbes that have been isolated from the human body;
2. Recruit a set of healthy donors and obtain samples from a set of body regions
3. Perform initial 16S rDNA gene metagenomic sequence analyses to estimate the complexity of the microbiota at these sites.

Centers: Baylor, Broad, JCVI, WUSTL

• ~10times more bateria cells than human cells in the body
• small-subunit (16S) ribosomal RNA gene-sequence-based surveys:

 * found in all microorganisms 
 * has enough sequence conservation for accurate alignment 
 * has enough variation for phylogenetic analyses.

• skin, mouth, oesophagus, stomach, colon and vagina
• largest reported data sets are for the gut
• most of the 10–100 trillion microorganisms in the human gastrointestinal tract live in the colon.
• more than 90% of all phylogenetic types (phylotypes) of colonic bacteria belong to just 2 of the 70 known divisions (phyla) in the domain Bacteria: the Firmicutes and the Bacteroidetes.

Firmicutes (Gram-positive bacteria) : 639 Genome Sequences

   * Bacilli    472
   * Clostridia    106
   * Erysipelotrichi    1
   * Mollicutes    60
   * Thermolithobacteria   
   * unclassified Firmicutes sensu stricto   
   * environmental samples    

Bacteroidetes : 53 Genome Sequences

   * Bacteroidetes (class)    22
   * Flavobacteria    21
   * Sphingobacteria    8
   * unclassified Bacteroidetes    1
   * environmental samples    1

Actinobacteria

• In colon, the differences between individuals are greater than the differences between different sampling sites in one individuall
• Comunirties are usually stable over time

SIMHC

Data

Online

• 113 reference genomes : 89 complete, 24 incomplete

         #elem   min     max     mean    median  n50     sum
 NC_     173     3361    8264687 2184609 1966858 4317977 377,937,361   # come from 89 genomes ; some contain plasmids
 NZ_     3505    185     1802798 26389   9051    73891   92,494,763    # come from 24 genomes
 total   3678    185     8264687 127904  9940    3561584 470,432,124

• 118084 Sanger reads from 3 insert libs (small,med,large)

 #reads  min     max     mean    median  n50     sum
 116771  43      3754    950     968     982     110875383

• More than 50% of reads are from Proteobacteria; Gammaproteobacteria

 Proteobacteria  73261
 Firmicutes      15707
 Actinobacteria  10744
 ...

• read coverage of each organism 0.09 ..0.53X

 0.53X: Moorella thermoacetica ATCC 39073 (1426 reads; NC_007644 2,628,784bp 55.79%GC) (Firmicutes)
 0.09X: Xylella fastidiosa Ann-1

Local

• 113 reference genomes : 89 complete, 24 incomplete
• 116771 Sanger reads from 3 insert libs (small,med,large)
• 118084-116771=1313 Moorella and Xylella were discarded !!!
• read coverage of each organism ...

 0.23X: Moorella thermoacetica ATCC 39073 (740 reads; NC_007644 2,628,784bp 55.79%GC) (Firmicutes)

Assemblies

Contig stats

              #elem   min     max     mean    median  n50     sum             singl

 phrap-ctg    23398   73      8603    1289    1194    1341    30,163,430      66524
 arachne-ctg  578     240     6300    1878    1822    1985    1,085,508       115300
 jazz-scaff   860     1000    39837   3236    1105    7278    2,783,247       109080

 CA-scaff     4327    1000    48,861  1682    1342    1456    7,278,044       76270     # OBT trimming of the reads
 CA-ctg       4491    1000    5252    1419    1340    1388    6,374,863                 # 4407 CONTAINED in references
 CA-deg       11611   66      5920    850     833     898     9,865,902

 AMOS-ctg     95372   72      7426    975     916     964     92,959,055      5661      # alignment based trimming of the reads; casm-layout "-S -r" have been used
 minimus2-ctg 15211   85      4699    1257    1205    1305    19,119,413      82535     # alignment based trimming of the reads